X-37591763-A-T

Position:

• chrX-37591763-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001170331.2(LANCL3):​c.573+19320A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (1682 hom., 5313 hem., cov: 20)
• Consequence: LANCL3 NM_001170331.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

Genes affected

LANCL3 (HGNC:24767): (LanC like family member 3) Predicted to be involved in carbohydrate metabolic process. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LANCL3	NM_001170331.2	c.573+19320A>T		intron_variant		ENST00000378619.4
LANCL3	NM_198511.3	c.573+19320A>T		intron_variant
LANCL3	XM_011543904.3	c.27+18896A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LANCL3	ENST00000378619.4	c.573+19320A>T		intron_variant		1	NM_001170331.2	P1
LANCL3	ENST00000378621.7	c.573+19320A>T		intron_variant		1
LANCL3	ENST00000614025.4	c.573+19320A>T		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.199 AC: 20487 AN: 103074 Hom.: 1682 Cov.: 20 AF XY: 0.196 AC XY: 5306 AN XY: 27110

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.222

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.199 AC: 20483 AN: 103112 Hom.: 1682 Cov.: 20 AF XY: 0.196 AC XY: 5313 AN XY: 27156

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.218

Alfa AF: 0.186 Hom.: 911

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11266282; hg19: chrX-37451016;